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Predicted mouse peroxisome-targeted proteins and their actual subcellular locations.


ABSTRACT:

Background

The import of most intraperoxisomal proteins is mediated by peroxisome targeting signals at their C-termini (PTS1) or N-terminal regions (PTS2). Both signals have been integrated in subcellular location prediction programs. However their present performance, particularly of PTS2-targeting did not seem fitting for large-scale screening of sequences.

Results

We modified an earlier reported PTS1 screening method to identify PTS2-containing mouse candidates using a combination of computational and manual annotation. For rapid confirmation of five new PTS2- and two previously identified PTS1-containing candidates we developed the new cell line CHO-perRed which stably expresses the peroxisomal marker dsRed-PTS1. Using CHO-perRed we confirmed the peroxisomal localization of PTS1-targeted candidate Zadh2. Preliminary characterization of Zadh2 expression suggested non-PPARalpha mediated activation. Notably, none of the PTS2 candidates located to peroxisomes.

Conclusion

In a few cases the PTS may oscillate from "silent" to "functional" depending on its surface accessibility indicating the potential for context-dependent conditional subcellular sorting. Overall, PTS2-targeting predictions are unlikely to improve without generation and integration of new experimental data from location proteomics, protein structures and quantitative Pex7 PTS2 peptide binding assays.

SUBMITTER: Mizuno Y 

PROVIDER: S-EPMC2638156 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature

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Publications

Predicted mouse peroxisome-targeted proteins and their actual subcellular locations.

Mizuno Yumi Y   Kurochkin Igor V IV   Herberth Marlis M   Okazaki Yasushi Y   Schönbach Christian C  

BMC bioinformatics 20081212


<h4>Background</h4>The import of most intraperoxisomal proteins is mediated by peroxisome targeting signals at their C-termini (PTS1) or N-terminal regions (PTS2). Both signals have been integrated in subcellular location prediction programs. However their present performance, particularly of PTS2-targeting did not seem fitting for large-scale screening of sequences.<h4>Results</h4>We modified an earlier reported PTS1 screening method to identify PTS2-containing mouse candidates using a combinat  ...[more]

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